library(rdt)
pdir <- './prov_samples'
prov.init(save.debug = T, prov.dir = './prov_samples', annotate.inside.functions = T, overwrite = F)
library(modleR)
library(sp)
species <- names(example_occs)
occs <- example_occs[[1]]
test_folder <- "~/Dropbox/Reproducibility/prov2repr/prov_samples/modler_results"
sdmdata_1sp <- modleR::setup_sdmdata(species_name = species[1],
occurrences = occs,
predictors = example_vars,
models_dir = test_folder,
partition_type = "crossvalidation",
cv_partitions = 5,
cv_n = 1,
buffer_type = "mean",
png_sdmdata = F,
n_back = 500,
clean_dupl = FALSE,
clean_uni = FALSE,
clean_nas = FALSE,
geo_filt = FALSE,
geo_filt_dist = 10,
select_variables = TRUE,
sample_proportion = 0.5,
cutoff = 0.7)
many <- modleR::do_many(species_name = species[1],
predictors = example_vars,
models_dir = test_folder,
png_partitions = F,
write_bin_cut = FALSE,
write_rda = TRUE,
bioclim = FALSE,
domain = FALSE,
glm = FALSE,
svmk = FALSE,
svme = FALSE,
maxnet = F,
rf = F,
mahal = FALSE,
brt = TRUE,
equalize = TRUE)
#file_in('./results/')),
fm <- modleR::final_model(species_name = species[1],
algorithms = NULL, #if null it will take all the algorithms in disk
models_dir = test_folder,
which_models = c("raw_mean",
"bin_mean",
"bin_consensus"),
consensus_level = 0.5,
uncertainty = TRUE,
overwrite = TRUE, png_final = F)
ens <- modleR::ensemble_model(species_name = species[1],
occurrences = occs,
performance_metric = "pROC",
which_ensemble = c("average",
"best",
"frequency",
"weighted_average",
"median",
"pca",
"consensus"),
consensus_level = 0.5,
which_final = "raw_mean",
models_dir = test_folder,
overwrite = TRUE, png_ensemble = F)
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